No differences that I can find: same template, tags, formatting, etc. Sometimes deleting and recreating the anchored frame will fix the issue, though in large documents this workaround is cumbersome and irritating.

Adobe Framemaker 11 version 11.0.2.384. It says all Adobe products are up to date. Yes, the PDF is generated from a book. Though this has happened with more than one book. The vanishing comments recur within the same FM file but are not limited to a single file. It can happen in multiple files within the same book. I should also add that regenerating the PDF changes nothing: the comments that were missing continue to be missing, the comments that were intact continue to be intact. Moreover i am not the only one here who has this issue. There are six of us and we all run into it periodically. We would be most grateful for any ideas.

I was mistaken. The tags at the frame insertion points were not all the same, and coincidentally some of the tags were missing from "Include Paragraphs" window on the Tags tab. Easy fix and now I feel stupid. Thanks all for the help.